Project ID: plumID:20.025
Name: The role of water in host-guest interaction
Archive: https://github.com/valeriorizzi/Deep-LDA_LigandBinding_SAMPL5/archive/refs/heads/main.zip
Category: bio
Keywords: ligand binding, water, opes, SAMPL5
PLUMED version: 2.5
Contributor: Valerio Rizzi
Submitted on: 14 Sep 2020
Last revised: 15 Jan 2021
Publication: V. Rizzi, L. Bonati, N. Ansari, M. Parrinello, The role of water in host-guest interaction. Nature Communications. 12 (2021)

PLUMED input files

File Compatible with
OAH_G1/plumed.dat tested on v2.8 tested on master
OAH_G2/plumed.dat tested on v2.8 tested on master
OAH_G3/plumed.dat tested on v2.8 tested on master
OAH_G4/plumed.dat tested on v2.8 tested on master
OAH_G5/plumed.dat tested on v2.8 tested on master
OAH_G6/plumed.dat tested on v2.8 tested on master
OAH_alone/plumed.dat tested on v2.8 tested on master
OAMe_G1/plumed.dat tested on v2.8 tested on master
OAMe_G2/plumed.dat tested on v2.8 tested on master
OAMe_G3/plumed.dat tested on v2.8 tested on master
OAMe_G4/plumed.dat tested on v2.8 tested on master
OAMe_G5/plumed.dat tested on v2.8 tested on master
OAMe_G6/plumed.dat tested on v2.8 tested on master
OAMe_alone/plumed.dat tested on v2.8 tested on master

Last tested: 27 Sep 2022, 18:19:49

Project description and instructions
This egg contains the input files for replicating ligand binding simulations from the SAMPL5 challenge with a Deep-LDA CV. The CV focuses on accelerating the water throughout the binding/unbinding events. For more information about Deep-LDA, we refer to plumID:20.004. The CVs were trained with Pytorch version 1.4 and the simulations were run with Gromacs 2019.4.

Submission history
[v1] 14 Sep 2020: original submission
[v2] 15 Jan 2021: updated doi

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plumeDnest:20.025